Proteins form structured aggregates known as amyloid fibrils. The
growth mechanisms of amyloid fibrils, which are implicated in a number
of neurodegenerative diseases, are poorly understood. We have
performed extensive all-atom molecular dynamics simulations to study
the structural changes that occur in a random coil protein fragment
from the yeast prion Sup35 and Aβ-peptide upon interaction with a
preformed fibril. We show that the random coil to β-strand transition
in the protein fragment as it becomes a part of the fibril occurs
abruptly over a very narrow time interval. Amyloid fibrils further
adopt a cross-β-spine structure in which the two β-sheets fully
interdigitate to create a dry interface. Formation of such a dry
interface is usually associated with self-assembly of extended
hydrophobic surfaces. We studied the role of water and mechanistic
differences in the dry interface formation between β-sheets formed
from vastly different peptide sequences, one a polar sequence from the
yeast prion Sup35 and the other a predominantly hydrophobic sequence
from the Aβ-peptide.